Dear Jeremy,

thanks for the reply!

Indeed, there's another feature I don't fully understand: I have a bgiWig
file that contains reads of only one chromosome. I expected that Circster
would display this one chromosome as one circle, but apparently Circster
always draws a circle where all possible chromosomes of a genome are
displayed. I think the usability would greatly increase if Circster only
displayed those chromosomes that are actually represented in the coverage
file. (Of course, I could zoom in, but if you're working with a chromosome
that's very small in comparison (e.g. the Y chromosome) the circular
representation is not really seen anymore as the region covered by the Y
chromosome is so tiny compared to the autosomes).

I hope this makes sense, let me know if there's already a solution for that
and I was just too blind to notice it!

Thanks a lot!

Best,

Friederike


2014-02-11 17:49 GMT+01:00 Jeremy Goecks <jgoe...@email.gwu.edu>:

> 1. I tested it using a bigWig and a BED file. Both were loaded nicely in
> Circos, but I was surprised to see that the visualization of both files
> looked exactly the same, i.e. both file types seemed to be interpreted as
> histograms/coverage data. From the Circos plots I've seen in publications,
> I assumed that BED files should be visualized as straight lines, indicating
> genome regions (rather than a coverage). Am I doing anything wrong? Or,
> rather, how should I modify the BED file so that its content is simply
> interpreted as genomic regions?
>
>
> This is a limitation of the visualization, and it should be
> addressed. I've created a Trello card for this enhancement that you follow
> here: https://trello.com/c/YIdx6QvV
>
> 2. In the Galaxy publication (www.biomedcentral.com/1471-2164/14/397),
> "line data" is mentioned for displaying connecting lines in the center of
> the circle - could you give me an example line of how this kind of data
> needs to be formatted?
>
>
> The format is a 7-column tabular file with tab-separated values:
>
> --
> chrom1 start1 end1 chrom2 start2 end2 score
> --
>
> Score isn't used right now, but it still needs to be there. Once you have
> this format, you'll need to convert the datatype from 'tabular' to 'chrint'
> in order to visualize it (click on the pencil icon --> Datatype. Also, I
> have a workflow up to convert Tophat fusion output data to chrint format
> here:
>
>  https://usegalaxy.org/u/jeremy/w/tophat-fusion-post-output-to-chrint
>
> Sorry for the cryptic nature of everything right now. We'll get this info
> and more up on a wiki page eventually (you're welcome to start one in the
> meantime). Let us know if you have more questions.
>
> Best,
> J.
>
>
>
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